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Path2Models: large-scale generation of computational models from biochemical pathway maps

Finja Büchel, Nicolas Rodriguez, Neil Swainston, Clemens Wrzodek, Tobias Czauderna, Roland Keller, Florian Mittag, Michael Schubert, Mihai Glont, Martin Golebiewski, Martijn van Iersel, Sarah Keating (+14 others)
2013 BMC Systems Biology  
Results: To increase the efficiency with which such models can be created, we automatically generated mathematical models from pathway representations using a suite of freely available software.  ...  Systems biology projects and omics technologies have led to a growing number of biochemical pathway reconstructions.  ...  Results Workflow from biochemical pathways to computational models In order to generate computational models from biological pathways on a large scale, a software pipeline composed of several steps that  ... 
doi:10.1186/1752-0509-7-116 pmid:24180668 pmcid:PMC4228421 fatcat:xihw5mql45gpzmiuc4svlr23nm

Metabolic Process Engineering for Biochemicals and Biofuels Production

Shang-Tian Yang
2014 Journal of Microbial & Biochemical Technology  
This is caused by the lack of a fundamental understanding of the interaction between cellular activities and fermentation Journal of Microbial & Biochemical Technology J o u rn al of M ic ro b ia l & Bioc  ...  However, the rational design of a metabolically engineered fermentation process to achieve high-productivity, highquality, and high-robustness is far behind in the biotechnology industry.  ...  The advantage of Path2Models database is that it can automatically generate mathematical model from pathway data sources, such as KEGG, Bio Carta, Meta Cyc and SABIO-RK.  ... 
doi:10.4172/1948-5948.1000e116 fatcat:czqxinhafnestk45asg76l7iyy

Curating and comparing 114 strain-specific genome-scale metabolic models of Staphylococcus aureus

Alina Renz, Andreas Dräger
2021 npj Systems Biology and Applications  
Recent advances in whole-genome sequencing and high-throughput techniques facilitate the generation of genome-scale metabolic models (GEMs).  ...  The scope of each model was evaluated, including the number of reactions, metabolites, and genes.  ...  More than 140,000 freely available and automatically generated mathematical models from pathway representations are available through the Path2Models project.  ... 
doi:10.1038/s41540-021-00188-4 pmid:34188046 fatcat:5ct762ktxzglhlotrgffknggaq

BioModels: Content, Features, Functionality, and Use

N Juty, R Ali, M Glont, S Keating, N Rodriguez, MJ Swat, SM Wimalaratne, H Hermjakob, N Le Novère, C Laibe, V Chelliah
2015 CPT: Pharmacometrics & Systems Pharmacology  
The resource provides access to over 1,200 models described in literature and over 140,000 models automatically generated from pathway resources.  ...  Most model components are cross-linked with external resources to facilitate interoperability. A large proportion of models are manually curated to ensure reproducibility of simulation results.  ...  This work received support from the Biotechnology and Biological Sciences Research Council (BioModels, BB/J019305/  ... 
doi:10.1002/psp4.3 pmid:26225232 pmcid:PMC4360671 fatcat:4ki3pd2zdze5pdvtqo4qhjbi3a

Metabolic pathway databases and model repositories

Abraham A. Labena, Yi-Zhou Gao, Chuan Dong, Hong-li Hua, Feng-Biao Guo
2017 Quantitative Biology  
at large.  ...  Besides, the automatically generated metabolic models that can be obtained from the model repositories are not accurate enough for further scientific usage without additional manual curation.  ...  Labena, Yi-Zhou Gao, Chuan Dong, Hong-li Hua and Feng-Biao Guo declare that they have no conflict of interest.  ... 
doi:10.1007/s40484-017-0108-3 fatcat:j6osebecqjehzj6lkchtldkwke

Integrated network analysis and effective tools in plant systems biology

Atsushi Fukushima, Shigehiko Kanaya, Kozo Nishida
2014 Frontiers in Plant Science  
We highlight (1) network visualization tools, (2) pathway analyses, (3) genome-scale metabolic reconstruction, and (4) the integration of high-throughput experimental data and mathematical models.  ...  Here we focus on the latest cutting-edge computational advances that facilitate their combination.  ...  from a large number of interactions (for example see Arabidopsis Interactome Mapping Consortium, 2011).  ... 
doi:10.3389/fpls.2014.00598 pmid:25408696 pmcid:PMC4219401 fatcat:v3vwvnflbncltg6eyo7kx6zwei

MEMOTE for standardized genome-scale metabolic model testing

Christian Lieven, Moritz E. Beber, Brett G. Olivier, Frank T. Bergmann, Meric Ataman, Parizad Babaei, Jennifer A. Bartell, Lars M. Blank, Siddharth Chauhan, Kevin Correia, Christian Diener, Andreas Dräger (+57 others)
2020 Nature Biotechnology  
MetaNetX consolidates biochemical namespaces by establishing a mapping between them through a set of unique identifiers.  ...  The opportunity to run pipelines locally during initial development and then to proceed seamlessly to large-scale computational resources in high-performance-computing or cloud settings provides users  ...  Sample size We aimed for the broadest possible assessment of publicly available genome-scale metabolic models. Sample size was therefore determined by the availability of data.  ... 
doi:10.1038/s41587-020-0446-y pmid:32123384 fatcat:pwhzzqyihvevzmz3jal6gm5zpy

Mimoza: web-based semantic zooming and navigation in metabolic networks

Anna Zhukova, David J Sherman
2015 BMC Systems Biology  
The complexity of genome-scale metabolic models makes them quite difficult for human users to read, since they contain thousands of reactions that must be included for accurate computer simulation.  ...  Metabolic network reconstruction and infrastructure There is a conflict between the level of detail of metabolic models needed for computer simulation and the one that can be easily analyzed by a human  ...  AZ was supported by a CORDI-S doctoral fellowship from Inria.  ... 
doi:10.1186/s12918-015-0151-5 pmid:25889977 pmcid:PMC4345040 fatcat:u4uechfjirc45omrc7ldjyg66m

SupraBiology 2014: Promoting UK-China collaboration on Systems Biology and High Performance Computing

Ettore Murabito, Riccardo Colombo, Chengkun Wu, Malkhey Verma, Samrina Rehman, Jacky Snoep, Shao-Liang Peng, Naiyang Guan, Xiangke Liao, Hans V. Westerhoff
2015 Quantitative Biology  
The event, sponsored by the "BBSRC China Partnering Awards" and ISBE, was organised as a sequence of talks addressing the different aspects of Systems Biology that can benefit from High Performance Computing  ...  A general discussion session followed where the scientific, technical, and logistic aspects of the prospected UK-China collaborations were examined.  ...  The automatic generation of a metabolic map can start either from prior knowledge of the pathways involved in the network (as in Path2Models [14] ), or just from the organism genome.  ... 
doi:10.1007/s40484-015-0039-9 fatcat:qu4tcgwuhfbfveg55e2vlzmbvy

ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis

Michael Römer, Johannes Eichner, Andreas Dräger, Clemens Wrzodek, Finja Wrzodek, Andreas Zell, Bin Liu
2016 PLoS ONE  
All tools are hosted on a customized Galaxy instance and run on a dedicated computation cluster. Users only need a web browser and an active internet connection in order to benefit from this service.  ...  Currently, the collection encompasses software for conversion and processing of community standards SBML and BioPAX, transcription factor analysis, and analysis of microarray data from transcriptomics  ...  BioPAX2SBML was used in the Path2Models project to create mathematical models in the SBML format from biochemical pathway maps retrieved from multiple data sources [12] .  ... 
doi:10.1371/journal.pone.0149263 pmid:26882475 pmcid:PMC4801062 fatcat:ast2kevfivab7hsxgxrxdj643i

Metabolomics, Standards, and Metabolic Modeling for Synthetic Biology in Plants

Camilla Beate Hill, Tobias Czauderna, Matthias Klapperstück, Ute Roessner, Falk Schreiber
2015 Frontiers in Bioengineering and Biotechnology  
In this article, we review challenges in the integration and analysis of large-scale metabolic data, present an overview of current bioinformatics methods for the modeling and visualization of metabolic  ...  Biochemical reactions are coordinated in metabolic pathways that interact in a complex way to allow adequate regulation.  ...  In addition, using a computational model can often generate a set of alternative strategies (Copeland et al., 2012) .  ... 
doi:10.3389/fbioe.2015.00167 pmid:26557642 pmcid:PMC4617106 fatcat:ojxxyeq4azfyhexwkvjic6f5m4

Quantitative and logic modelling of molecular and gene networks

Nicolas Le Novère
2015 Nature reviews genetics  
These initial conditions might affect the simulation results -for instance, in the case of systems with several stable states that can be reached from different trajectories.  ...  Quantitative models Mathematical models in which the values of the variables are determined by numerical analysis of the variables and parameters in the system.  ...  Froehlich for extensive reading and correction of the manuscript, to L. Stephens and S. Edelstein for their corrections and advice, and to C. Chaouiya, P. Mendes, J. Saez-Rodriguez and D.  ... 
doi:10.1038/nrg3885 pmid:25645874 pmcid:PMC4604653 fatcat:ewf5l5frsbfr3pu3ut5c4wcb6y

Automated inference of Boolean models from molecular interaction maps using CaSQ

Sara Sadat Aghamiri, Vidisha Singh, Aurélien Naldi, Tomáš Helikar, Sylvain Soliman, Anna Niarakis, Jinbo Xu
2020 Bioinformatics  
Computational modelling provides the means to study dynamic properties through in silico simulations and perturbations.  ...  The tool is able to process large and complex maps built with CellDesigner (either following SBGN standards or not) and produce Boolean models in a standard output format, SBML-qual, that can be further  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btaa484 pmid:32403123 pmcid:PMC7575051 fatcat:yy5nzo5nezdy3eqmqwwxhri6ca

Design considerations for representing systems biology information with the Systems Biology Graphical Notation

Falk Schreiber, Tobias Czauderna
2022 Journal of Integrative Bioinformatics  
Using the example of the Systems Biology Graphical Notation (SBGN) we will investigate design considerations for graphically presenting information from systems biology, in particular regarding the use  ...  of glyphs for types of information, the style of graph layout for network representation, and the concept of bricks for visual network creation.  ...  [104] , Path2Models [105] (a collection of models automatically generated from pathway resources), and LMME [106] (the Large Metabolic Model Explorer).  ... 
doi:10.1515/jib-2022-0024 pmid:35786424 pmcid:PMC9377698 fatcat:wpawq3olb5fk5octxjare5z2jm

Comparison of human cell signaling pathway databases—evolution, drawbacks and challenges

Saikat Chowdhury, Ram Rup Sarkar
2015 Database: The Journal of Biological Databases and Curation  
To advance this study, during the past two decades, systematic collections of pathway data from experimental studies have been compiled and distributed freely by several databases, which also integrate  ...  various computational tools for further analysis.  ...  Conflict of interest: None declared.  ... 
doi:10.1093/database/bau126 pmid:25632107 pmcid:PMC4309023 fatcat:b6y4vbdg7rfdrac5z3htaxdcji
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